A simple and efficient method was developed for the rapid screening and identification of ligands for monoamine oxidase B. A new ionic‐liquid‐based ultrasound‐assisted extraction method for medicinal herbs was also developed and validated. In addition, the hyphenated technique of countercurrent chromatography and semipreparative‐LC was developed and applied to the isolation of the chemical constituents for Pueraria thomsonii Benth. Three potent monoamine oxidase B inhibitors, namely, daidzein‐4′,7‐diglucoside (42.2 mg), puerarin 6′′‐O‐xyloside (88.3 mg), and 3′‐hydroxypuerarin (48.5 mg) with purities of 98.2, 96.3, and 97.1%, respectively, were obtained from 500 g of P. thomsonii raw material using semi‐preparative high‐performance liquid chromatography, whereas 3′‐methoxypuerarin (76.2 mg), daidzein‐8‐C‐apiosyl (1→6) glucoside (84.2 mg), and tectorigenin (75.1 mg) with purities of 98.5, 96.4, and 96.8%, respectively, were obtained from 500 g raw material via countercurrent chromatography using a two‐phase solvent system comprising n‐hexane–ethyl acetate–methanol–water at a volume ratio of 1.85:1.00:0.86:3.69 (v/v/v/v). Then, the anti‐Alzheimer activity of the phytochemicals was assessed using a PC12 cell model. Treatment with tectorigenin, daidzein‐4′,7‐diglucoside, puerarin 6′′‐O‐xyloside, 3′‐hydroxypuerarin, 3′‐methoxypuerarin, and daidzein‐8‐C‐apiosyl (1→6) glucoside (100 μg/mL), resulted in cell viabilities of 69.00, 65.81, 59.69, 57.90, 55.61, and 54.59%, respectively (p < 0.001). The protocol was proved to be very accurate and efficient.